The Swedish champions frustrated last season's European runners-up for a half in their first Group A match-up in Spain in October, before Diego Simeone's men exploded to life after the break to canter to a 5-0 victory.
The victory was the second of four straight for Atletico, who most recently downed Cordoba 4-2 on Saturday.
Simeone sent an ominous warning to Age Hareide's men, claiming the La Liga champions were still "improving" and "getting better".
"I think we are improving bit by bit, and we are getting better in our play," Simeone said, after their league win on Saturday.
"We have the chance of playing between the lines, which is good for our wide players as it allows them more space.
"Our style of play allows Raul Garcia, Mario Mandzukic and [Antoine] Griezmann to play nearer the box.
"As I have said before we are growing and today we shown some real class in our performance. A result like this is really good for the side."
Simeone reserved special praise for left winger Griezmann, who scored his first league goals for the club with a brace against Cordoba.
"Antoine Griezmann is working really well," Simeone said of the 23-year-old.
"He is growing day by day and he is getting rewards for his hard work. He played a very good match in all aspects of his play.
"I know you just see the goals, which are important for him and the team, but he shown some other aspects which were hugely beneficial to the team.
"His performance today was excellent and that is what we expect from him."
Despite scoring 12 goals in their past four wins in all competitions, and only failing to score once this term, Simeone encouraged his side to "score more goals".
"I think we need to look at it in the long term," Simeone said of criticism of their early season form.
"We made a lot of signings and we started the season winning the Spanish Cup.
"But we didn't play well in the match against Valencia and the first 10 minutes against Olympiakos in Greece.
"We have been average in some games and good in other matches.
"We need to score more goals, not just from the kickoff but throughout the whole game."
Since their breakthrough win over Olympiacos, Malmo have won two and lost two league games - along with their thrashing at the hands of Atletico.
Since his match-winning brace against the Greek champions, Markus Rosenberg has scored in three of five fixtures and will be their greatest threat to penetrate Atletico's defence at the Swedbank Stadion.
